The whole reason why they'll run cool without that restrictor, is that these engines run a 'reverse' thermostat. Instead of the tstat being on the output side of the water pump, it's on the inlet. Which means that the radiator is pressurized by the water pump the second the engine is turned on.
There's a bleed-tube on the top-pass side of the radiator that returns to the overflow tank. The end result being, there's always a little bit of coolant going through the radiator. Usually this is a net benefit - the system self bleeds, and does so very quickly. However if that restrictor is not in place, there will be more than a little coolant going through the radiator, wicking away more heat than was intended in the design. So no restrictor = too much flow through the self-bleed = too much flow through the radiator = cold
Now with that said... These systems are flippin' weird in that it uses the heater core lines to control the thermostat. So if your heater cores are clogged, or if you did a lazy bypass and just capped hoses - there won't be enough coolant going over the t-stat to appropriately regulate temperatures, and you'll get an overheat / hot condition even if everything else in the system works perfectly. This also goes for a partial clog. So if, for whatever reason, you wanted to bypass your heater core - you would loop a piece of hose around and just connect the waterpump to itself, NOT cap it off.
Couple bits come to mind, in no particular order
1. If you get heat when revved, the water pump is spinning. It's not air locked.
2. Double check coolant level in your reservoir. Low coolant is the first thing I'd be looking at here. Especially if you get any gurgling / waterfall type sounds from under the dash.
3. Verify your belt isn't slipping. From a cold start - let it run for a minute or two. Turn the engine off. Then go ***** the pulleys. Are any of them warm/hot?
4. How's that water pump looking anyway? I've seen some realllll bad aftermarkets. Some have a raw pump with no vane guide. Those are lame. My favorite was one that didn't even have an impeller on it... oops....
5. You can try back flushing your heater core. Disconnect the hoses and put a garden hose on it. The port on the rear of the engine is the outlet to the heater, front is the inlet to the pump